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Chiarelli DP, Sharma BD, Hon S, Bergamo LW, Lynd LR, Olson DG. Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metab Eng Commun 2024; 19:e00243. [PMID: 39040142 PMCID: PMC11260334 DOI: 10.1016/j.mec.2024.e00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.
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Affiliation(s)
- Daniela Prates Chiarelli
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bishal Dev Sharma
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Luana Walravens Bergamo
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lee R. Lynd
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G. Olson
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Liu Y, Li H, Liu W, Ren K, Li X, Zhang Z, Huang R, Han S, Hou J, Pan C. Bioturbation analysis of microbial communities and flavor metabolism in a high-yielding cellulase Bacillus subtilis biofortified Daqu. Food Chem X 2024; 22:101382. [PMID: 38665634 PMCID: PMC11043814 DOI: 10.1016/j.fochx.2024.101382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, a fortified Daqu (FF Daqu) was prepared using high cellulase-producing Bacillus subtilis, and the effects of in situ fortification on the physicochemical properties, flavor, active microbial community and metabolism of Daqu were analyzed. The saccharification power, liquefaction power, and cellulase activity of the FF Daqu were significantly increased compared with that of the traditional Daqu (CT Daqu). The overall differences in flavor components and their contents were not significant, but the higher alcohols were lower in FF Daqu. The relative abundance of dominant active species in FF Daqu was 85.08% of the total active microbiota higher than 63.42% in CT Daqu, and the biomarkers were Paecilomyces variotii and Aspergillus cristatus, respectively. The enzymes related to starch and sucrose metabolic pathways were up-regulated and expressed in FF Daqu. In the laboratory level simulation of baijiu brewing, the yield of baijiu was increased by 3.36% using FF Daqu.
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Affiliation(s)
- Yanbo Liu
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Liquor Style Engineering Technology Research Center, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Province Brewing Special Grain Development and Application Engineering Research Center, Zhengzhou 450046, China
- Zhengzhou Key Laboratory of Liquor Brewing Microbial Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Haideng Li
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Wenxi Liu
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Liquor Style Engineering Technology Research Center, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Province Brewing Special Grain Development and Application Engineering Research Center, Zhengzhou 450046, China
- Zhengzhou Key Laboratory of Liquor Brewing Microbial Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Kejin Ren
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Liquor Style Engineering Technology Research Center, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Province Brewing Special Grain Development and Application Engineering Research Center, Zhengzhou 450046, China
- Zhengzhou Key Laboratory of Liquor Brewing Microbial Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Xuehan Li
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Liquor Style Engineering Technology Research Center, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Province Brewing Special Grain Development and Application Engineering Research Center, Zhengzhou 450046, China
- Zhengzhou Key Laboratory of Liquor Brewing Microbial Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Zhenke Zhang
- Henan Yangshao Distillery Co., Ltd., Mianchi 472400, China
| | - Runna Huang
- Henan Yangshao Distillery Co., Ltd., Mianchi 472400, China
| | - Suna Han
- Henan Yangshao Distillery Co., Ltd., Mianchi 472400, China
| | - Jianguang Hou
- Henan Yangshao Distillery Co., Ltd., Mianchi 472400, China
| | - Chunmei Pan
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Liquor Style Engineering Technology Research Center, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- Henan Province Brewing Special Grain Development and Application Engineering Research Center, Zhengzhou 450046, China
- Zhengzhou Key Laboratory of Liquor Brewing Microbial Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
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3
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Daley SR, Kirby S, Sparling R. Adaptive evolution of Clostridium thermocellum ATCC 27405 on alternate carbon sources leads to altered fermentation profiles. Can J Microbiol 2024. [PMID: 38832648 DOI: 10.1139/cjm-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Consolidated bioprocessing candidate, Clostridium thermocellum, is a cellulose hydrolysis specialist, with the ability to ferment the released sugars to produce bioethanol. C. thermocellum is generally studied with model substrates Avicel and cellobiose to understand the metabolic pathway leading to ethanol. In the present study, adaptive laboratory evolution, allowing C. thermocellum DSM 1237 to adapt to growth on glucose, fructose, and sorbitol, with the prospect that some strains will adapt their metabolism to yield more ethanol. Adaptive growth on glucose and sorbitol resulted in an approximately 1 mM and 2 mM increase in ethanol yield per millimolar glucose equivalent, respectively, accompanied by a shift in the production of the other expected fermentation end products. The increase in ethanol yield observed for sorbitol adapted cells was due to the carbon source being more reduced compared to cellobiose. Glucose and cellobiose have similar oxidation states thus the increase in ethanol yield is due to the rerouting of electrons from other reduced metabolic products excluding H2 which did not decrease in yield. There was no increase in ethanol yield observed for fructose adapted cells, but there was an unanticipated elimination of formate production, also observed in sorbitol adapted cells suggesting that fructose has regulatory implications on formate production either at the transcription or protein level.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Kirby
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
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Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
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6
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Verrone V, Gupta A, Laloo AE, Dubey RK, Hamid NAA, Swarup S. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167757. [PMID: 37852479 DOI: 10.1016/j.scitotenv.2023.167757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.
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Affiliation(s)
- Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore.
| | - Andrew Elohim Laloo
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Nur Ashikin Abdul Hamid
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Sanjay Swarup
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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7
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Wang X, Jiang Y, Liu H, Yuan H, Huang D, Wang T. Research progress of multi-enzyme complexes based on the design of scaffold protein. BIORESOUR BIOPROCESS 2023; 10:72. [PMID: 38647916 PMCID: PMC10992622 DOI: 10.1186/s40643-023-00695-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/04/2023] [Indexed: 04/25/2024] Open
Abstract
Multi-enzyme complexes designed based on scaffold proteins are a current topic in molecular enzyme engineering. They have been gradually applied to increase the production of enzyme cascades, thereby achieving effective biosynthetic pathways. This paper reviews the recent progress in the design strategy and application of multi-enzyme complexes. First, the metabolic channels in the multi-enzyme complex have been introduced, and the construction strategies of the multi-enzyme complex emerging in recent years have been summarized. Then, the discovered enzyme cascades related to scaffold proteins are discussed, emphasizing on the influence of the linker on the fusion enzyme (fusion protein) and its possible mechanism. This review is expected to provide a more theoretical basis for the modification of multi-enzyme complexes and broaden their applications in synthetic biology.
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Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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Xiao Y, Dong S, Liu YJ, You C, Feng Y, Cui Q. Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum. Int J Biol Macromol 2023; 250:126226. [PMID: 37558019 DOI: 10.1016/j.ijbiomac.2023.126226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.
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Affiliation(s)
- Yan Xiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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9
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Wang X, Jiang Y, Liu H, Zhang X, Yuan H, Huang D, Wang T. In vitro assembly of the trehalose bi-enzyme complex with artificial scaffold protein. Front Bioeng Biotechnol 2023; 11:1251298. [PMID: 37711449 PMCID: PMC10497880 DOI: 10.3389/fbioe.2023.1251298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction: Trehalose is a significant rare sugar known for its stable properties and ability to protect biomolecules from environmental factors. Methods: In this study, we present a novel approach utilizing a scaffold protein-mediated assembly method for the formation of a trehalose bi-enzyme complex. This complex consists of maltooligosyltrehalose synthase (MTSase) and maltooligosyltrehalose trehalohydrolase (MTHase), which work in tandem to catalyze the substrate and enhance the overall catalytic efficiency. Utilizing the specific interaction between cohesin and dockerin, this study presents the implementation of an assembly, an analysis of its efficiency, and an exploration of strategies to enhance enzyme utilization through the construction of a bi-enzyme complex under optimal conditions in vitro. Results and Discussion: The bi-enzyme complex demonstrated a trehalose production level 1.5 times higher than that of the free enzyme mixture at 40 h, with a sustained upward trend. Compared to free enzyme mixtures, the adoption of a scaffold protein-mediated bi-enzyme complex may improve cascade reactions and catalytic effects, thus presenting promising prospects.
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Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyi Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
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10
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Young ES, Butler JD, Molesworth-Kenyon SJ, Kenyon WJ. Biofilm-Mediated Fragmentation and Degradation of Microcrystalline Cellulose by Cellulomonas flavigena KU (ATCC 53703). Curr Microbiol 2023; 80:200. [PMID: 37129770 DOI: 10.1007/s00284-023-03309-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Cellulomonas flavigena KU (ATCC 53703) produces an extracellular matrix involved in the degradation of microcrystalline cellulose. This extracellular material is primarily composed of the gel-forming, β-1,3-glucan known as curdlan and associated, cellulose-degrading enzymes. In this study, the effects of various forms of nutrient limitation on cellulose attachment, cellular aggregation, curdlan production, and biofilm formation were investigated throughout a 7-day incubation period by using phase-contrast microscopy. Compared to cultures grown in non-limiting media, nitrogen-limitation promoted early attachment of C. flavigena KU cells to the cellulose surface, and cellulose attachment was congruent with cellular aggregation and curdlan production. Over the course of the experiment, microcolonies of attached cells grew into curdlan-producing biofilms on the cellulose. By contrast, bacterial cells grown on cellulose in non-limiting media remained unattached and unaggregated throughout most of the incubation period. By 7 days of incubation, bacterial aggregation was ninefold greater in N-limited cultures compared to nutritionally complete cultures. In a similar way, phosphorus- and vitamin-limitation (i.e., yeast extract-limitation) also resulted in early cellulose attachment and biofilm formation. Furthermore, nutrient limitation promoted more rapid and efficient fragmentation and degradation of cellulose, with cellulose fragments in low-N media averaging half the size of those in high-N media after 7 days. Two modes of cellulose degradation are proposed for C. flavigena KU, a "planktonic mode" and a "biofilm mode". Similar observations have been reported for other curdlan-producing cellulomonads, and these differing cellulose degradation strategies may ultimately prove to reflect sequential stages of a multifaceted biofilm cycle important in the bioconversion of this abundant and renewable natural resource.
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Affiliation(s)
- Emma S Young
- Biology Program, Department of Natural Sciences, University of West Georgia, Carrollton, GA, 30118, USA
| | - John D Butler
- Biology Program, Department of Natural Sciences, University of West Georgia, Carrollton, GA, 30118, USA
| | - Sara J Molesworth-Kenyon
- Biology Program, Department of Natural Sciences, University of West Georgia, Carrollton, GA, 30118, USA
| | - William J Kenyon
- Biology Program, Department of Natural Sciences, University of West Georgia, Carrollton, GA, 30118, USA.
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11
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Uke A, Sornyotha S, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Genomic analysis of Paenibacillus macerans strain I6, which can effectively saccharify oil palm empty fruit bunches under nutrient-free conditions. J Biosci Bioeng 2023:S1389-1723(23)00111-1. [PMID: 37095007 DOI: 10.1016/j.jbiosc.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
The improper disposal of palm oil industrial waste has led to serious environmental pollution. In this study, we isolated Paenibacillus macerans strain I6, which can degrade oil palm empty fruit bunches generated by the palm oil industry in nutrient-free water, from bovine manure biocompost and sequenced its genome on PacBio RSII and Illumina NovaSeq 6000 platforms. We obtained 7.11 Mbp of genomic sequences with 52.9% GC content from strain I6. Strain I6 was phylogenetically closely related to P. macerans strains DSM24746 and DSM24 and was positioned close to the head of the branch containing strains I6, DSM24746, and DSM24 in the phylogenetic tree. We used the RAST (rapid annotation using subsystem technology) server to annotate the strain I6 genome and discovered genes related to biological saccharification; 496 genes were related to carbohydrate metabolism and 306 genes were related to amino acids and derivatives. Among them were carbohydrate-active enzymes (CAZymes), including 212 glycoside hydrolases. Up to 23.6% of the oil palm empty fruit bunches was degraded by strain I6 under anaerobic and nutrient-free conditions. Evaluation of the enzymatic activity of extracellular fractions of strain I6 showed that amylase and xylanase activity was highest when xylan was the carbon source. The high enzyme activity and the diversity in the associated genes may contribute to the efficient degradation of oil palm empty fruit bunches by strain I6. Our results indicate the potential utility of P. macerans strain I6 for lignocellulosic biomass degradation.
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Affiliation(s)
- Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Somphit Sornyotha
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Sirilak Baramee
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.
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12
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Ye C, Geng S, Zhang Y, Qiu H, Zhou J, Zeng Q, Zhao Y, Wu D, Yu G, Gong H, Hu B, Hong Y. The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis). Anim Microbiome 2023; 5:20. [PMID: 37005679 PMCID: PMC10067185 DOI: 10.1186/s42523-023-00239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. RESULTS Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. CONCLUSIONS Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.
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Affiliation(s)
- Chen Ye
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Shiyu Geng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yingyu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Qi Zeng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yafei Zhao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Guilan Yu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Haibo Gong
- Jiangxi Provincial Aquatic Biology Protection and Rescue Center, Nanchang, 330000, China
| | - Beijuan Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
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13
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Wang J, Zhuang Y, Song X, Lin X, Wang X, Yang F, Chen X. Differential transcriptome analysis of Sporocytophaga sp. CX11 and identification of candidate genes involved in lignocellulose degradation. BIORESOUR BIOPROCESS 2023; 10:8. [PMID: 38647554 PMCID: PMC10992098 DOI: 10.1186/s40643-023-00629-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
Cellulose is the most abundant renewable bioresources on earth, and the biodegradation and utilization of cellulose would contribute to the sustainable development of global environment. Sporocytophaga species are common aerobic cellulose-degrading bacteria in soil, which can adhere to the surface of cellulose matrix and motile by gliding. In this study, a differential transcriptome analysis of Sporocytophaga sp. CX11 was performed and a total of 4,217 differentially expressed genes (DEGs) were identified. Gene Ontology enrichment results showed that there are three GO categories related to cellulose degradation function among the annotated DEGs. A total of 177 DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes), among which 54 significantly upregulated CAZymes were mainly cellulases, hemicellulases, pectinases, etc. 39 DEGs were screened to associate with gliding function. In order to explore unannotated genes potentially related to cellulose metabolism, cluster analysis was performed using the Short-Time Series Expression Miner algorithm (STEM). 281 unannotated genes were predicted to be associated with the initial-middle stage of cellulose degradation and 289 unannotated genes might function in the middle-last stage of cellulose degradation. Sporocytophaga sp. CX11 could produce extracellular endo-xylanase, endo-glucanase, FPase and β-glucosidase, respectively, according to different carbon source conditions. Altogether, this study provides valuable insights into the transcriptome information of Sporocytophaga sp. CX11, which would be useful to explore its application in biodegradation and utilization of cellulose resources.
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Affiliation(s)
- Jiwei Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Ying Zhuang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xianghe Song
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xu Lin
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xiangyi Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
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14
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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15
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Yang C, Liu W, Chen S, Zong X, Yuan P, Chen X, Li X, Li Y, Xue W, Dai J. MOF-Immobilized Two-in-One Engineered Enzymes Enhancing Activity of Biocatalytic Cascade for Tumor Therapy. Adv Healthc Mater 2023; 12:e2203035. [PMID: 36661124 DOI: 10.1002/adhm.202203035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/04/2023] [Indexed: 01/21/2023]
Abstract
Biocatalytic systems based on enzyme cascade reactions have attracted growing interest in the field of biocatalytic medicine. However, it is a major challenge to reasonably construct enzyme cascade reactions with high stability, selectivity, and catalytic efficiency for the in vivo biocatalytic application. Herein, two-in-one engineered glucose oxidase (GOx-Fe0 ) is fabricated by a biomineralization strategy, through which a nanozyme (Fe0 NP) is anchored within the inner cavity of GOx. Then, GOx-Fe0 is immobilized in a pH-sensitive metal-organic framework (MOF) zeolitic imidazolate framework-8 (ZIF-8) to establish a stable and effective MOF-immobilized two-in-one engineered enzyme, GOx-Fe0 @ZIF-8. In vitro studies show that GOx-Fe0 @ZIF-8 exhibits excellent stability and high pH/glucose selectivity, and the shorter spacing between cascade enzymes can increase the cascade throughput and effectively improve the reaction efficiency of the enzyme cascade. In vivo experiments exhibit that GOx-Fe0 @ZIF-8 solves the instability and systemic toxicity of free enzymes, and achieves deep tumor penetration and significant chemodynamic therapeutic efficacy through a pH/glucose-selective enzyme cascade reaction in tumor site. Taken together, such an orchestrated enzyme engineering strategy can effectively improve enzyme stability, selectivity, and enzyme cascade reaction efficiency via chemical transformations, and also provide a promising strategy for the application of biocatalytic cascade reactions in vivo.
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Affiliation(s)
- Caiqi Yang
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Wen Liu
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Shanfeng Chen
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Xiaoqing Zong
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Pengfei Yuan
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Xinjie Chen
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Xiaodi Li
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Yuchao Li
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Wei Xue
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
| | - Jian Dai
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Engineering Technology Research Center of Drug Carrier of Guangdong, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
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16
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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17
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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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18
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Moraïs S, Stern J, Artzi L, Fontes CMGA, Bayer EA, Mizrahi I. Carbohydrate Depolymerization by Intricate Cellulosomal Systems. Methods Mol Biol 2023; 2657:53-77. [PMID: 37149522 DOI: 10.1007/978-1-0716-3151-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cellulosomes are multi-enzymatic nanomachines that have been fine-tuned through evolution to efficiently deconstruct plant biomass. Integration of cellulosomal components occurs via highly ordered protein-protein interactions between the various enzyme-borne dockerin modules and the multiple copies of the cohesin modules located on the scaffoldin subunit. Recently, designer cellulosome technology was established to provide insights into the architectural role of catalytic (enzymatic) and structural (scaffoldin) cellulosomal constituents for the efficient degradation of plant cell wall polysaccharides. Owing to advances in genomics and proteomics, highly structured cellulosome complexes have recently been unraveled, and the information gained has inspired the development of designer-cellulosome technology to new levels of complex organization. These higher-order designer cellulosomes have in turn fostered our capacity to enhance the catalytic potential of artificial cellulolytic complexes. In this chapter, methods to produce and employ such intricate cellulosomal complexes are reported.
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Affiliation(s)
- Sarah Moraïs
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Edward A Bayer
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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19
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Cytochromes P450 in biosensing and biosynthesis applications: Recent progress and future perspectives. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Tsai SL, Sun Q, Chen W. Advances in consolidated bioprocessing using synthetic cellulosomes. Curr Opin Biotechnol 2022; 78:102840. [PMID: 36356377 DOI: 10.1016/j.copbio.2022.102840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
The primary obstacle impeding the more widespread use of biomass for energy and chemical production is the absence of a low-cost technology for overcoming their recalcitrant nature. It has been shown that the overall cost can be reduced by using a 'consolidated' bioprocessing (CBP) approach, in which enzyme production, biomass hydrolysis, and sugar fermentation can be combined. Cellulosomes are enzyme complexes found in many anaerobic microorganisms that are highly efficient for biomass depolymerization. While initial efforts to display synthetic cellulosomes have been successful, the overall conversion is still low for practical use. This limitation has been partially alleviated by displaying more complex cellulsome structures either via adaptive assembly or by using synthetic consortia. Since synthetic cellulosome nanostructures have also been created using either protein nanoparticles or DNA as a scaffold, there is the potential to tether these nanostructures onto living cells in order to further enhance the overall efficiency.
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Affiliation(s)
- Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City 106335, Taiwan
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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Dorival J, Moraïs S, Labourel A, Rozycki B, Cazade PA, Dabin J, Setter-Lamed E, Mizrahi I, Thompson D, Thureau A, Bayer EA, Czjzek M. Mapping the deformability of natural and designed cellulosomes in solution. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:68. [PMID: 35725490 PMCID: PMC9210761 DOI: 10.1186/s13068-022-02165-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/08/2022] [Indexed: 12/02/2022]
Abstract
Background Natural cellulosome multi-enzyme complexes, their components, and engineered ‘designer cellulosomes’ (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes, but the modular architecture challenges structure determination and rational design. Results We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of Rg and Dmax values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution. Conclusions Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02165-3.
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Liu Y, Angelov A, Feiler W, Baudrexl M, Zverlov V, Liebl W, Vanderhaeghen S. Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:121. [PMID: 36371193 PMCID: PMC9655821 DOI: 10.1186/s13068-022-02216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited. RESULTS In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan). CONCLUSIONS We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Werner Feiler
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Sonja Vanderhaeghen
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: IMGM Laboratories, Lochhamer Straße 29a, 82152 Planegg, Germany
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Ayuso-Fernández I, Molpeceres G, Camarero S, Ruiz-Dueñas FJ, Martínez AT. Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1003489. [PMID: 37746217 PMCID: PMC10512382 DOI: 10.3389/ffunb.2022.1003489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/22/2022] [Indexed: 09/26/2023]
Abstract
The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. ASR allows the subsequent resurrection in the laboratory of inferred proteins from now extinct organisms, becoming an outstanding tool to study enzyme evolution. Here we review the recent advances in ASR methods and their application to study fungal evolution, with special focus on wood-decay fungi as essential organisms in the global carbon cycling.
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Affiliation(s)
- Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
| | | | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
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Glycosyltransferase-Related Protein GtrA Is Essential for Localization of Type IX Secretion System Cargo Protein Cellulase Cel9A and Affects Cellulose Degradation in Cytophaga hutchinsonii. Appl Environ Microbiol 2022; 88:e0107622. [PMID: 36197104 PMCID: PMC9599414 DOI: 10.1128/aem.01076-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Cytophaga hutchinsonii digests cellulose through a novel cellulose degradation mechanism. It possesses the lately characterized type IX secretion system (T9SS). We recently discovered that N-glycosylation of the C-terminal domain (CTD) of a hypothetical T9SS substrate protein in the periplasmic space of C. hutchinsonii affects protein secretion and localization. In this study, green fluorescent protein (GFP)-CTDCel9A recombinant protein was found with increased molecular weight in the periplasm of C. hutchinsonii. Site-directed mutagenesis studies on the CTD of cellulase Cel9A demonstrated that asparagine residue 900 in the D-X-N-X-S motif is important for the processing of the recombinant protein. We found that the glycosyltransferase-related protein GtrA (CHU_0012) located in the cytoplasm of C. hutchinsonii is essential for outer membrane localization of the recombinant protein. The deletion of gtrA decreased the abundance of the outer membrane proteins and affected cellulose degradation by C. hutchinsonii. This study provided a link between the glycosylation system and cellulose degradation in C. hutchinsonii. IMPORTANCE N-Glycosylation systems are generally limited to some pathogenic bacteria in prokaryotes. The disruption of the N-glycosylation pathway is related to adherence, invasion, colonization, and other phenotypic characteristics. We recently found that the cellulolytic bacterium Cytophaga hutchinsonii also has an N-glycosylation system. The cellulose degradation mechanism of C. hutchinsonii is novel and mysterious; cellulases and other proteins on the cell surface are involved in utilizing cellulose. In this study, we identified an asparagine residue in the C-terminal domain of cellulase Cel9A that is necessary for the processing of the T9SS cargo protein. Moreover, the glycosyltransferase-related protein GtrA is essential for the localization of the GFP-CTDCel9A recombinant protein. Deletion of gtrA affected cellulose degradation and the abundance of outer membrane proteins. This study enriched the understanding of the N-glycosylation system in C. hutchinsonii and provided a link between N-glycosylation and cellulose degradation, which also expanded the role of the N-glycosylation system in bacteria.
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Duarte M, Alves VD, Correia M, Caseiro C, Ferreira LM, Romão MJ, Carvalho AL, Najmudin S, Bayer EA, Fontes CM, Bule P. Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies. Int J Biol Macromol 2022; 224:55-67. [DOI: 10.1016/j.ijbiomac.2022.10.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
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Kumar Saini J, Himanshu, Hemansi, Kaur A, Mathur A. Strategies to enhance enzymatic hydrolysis of lignocellulosic biomass for biorefinery applications: A review. BIORESOURCE TECHNOLOGY 2022; 360:127517. [PMID: 35772718 DOI: 10.1016/j.biortech.2022.127517] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Global interest in lignocellulosic biorefineries has increased in the recent past due to technological advancements in sustainable and cost-effective production of numerous commodity and speciality chemicals and fuels from renewable lignocellulosic biomass (LCB). As a result, the market value of biorefinery products has also increased over the time, with an estimated worth of USD 867.7 billion by 2025. However, biorefinery operations, especially enzymatic hydrolysis, suffer from many challenges that limits the cost-effectiveness of conversion of LCB. Therefore, it is essential to understand and address these challenges in future biorefineries. The paper focuses on recent trends and challenges in enzymatic hydrolysis of LCB during lignocellulosic biorefinery operation for greener synthesis of energy, fuels, chemicals and other high-value products. Insights into the gaps in knowledge and technological challenges have also been addressed together with focus on future research needs and perspectives of enzymatic hydrolysis of LCB for biorefinery applications.
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Affiliation(s)
- Jitendra Kumar Saini
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India.
| | - Himanshu
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Hemansi
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Research & Development Office, Ashoka University, Sonipat, Haryana PIN- 131029, India
| | - Amanjot Kaur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Aayush Mathur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
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Barzkar N, Babich O, Das R, Sukhikh S, Tamadoni Jahromi S, Sohail M. Marine Bacterial Dextranases: Fundamentals and Applications. Molecules 2022; 27:molecules27175533. [PMID: 36080300 PMCID: PMC9458216 DOI: 10.3390/molecules27175533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dextran, a renewable hydrophilic polysaccharide, is nontoxic, highly stable but intrinsically biodegradable. The α-1, 6 glycosidic bonds in dextran are attacked by dextranase (E.C. 3.2.1.11) which is an inducible enzyme. Dextranase finds many applications such as, in sugar industry, in the production of human plasma substitutes, and for the treatment and prevention of dental plaque. Currently, dextranases are obtained from terrestrial fungi which have longer duration for production but not very tolerant to environmental conditions and have safety concerns. Marine bacteria have been proposed as an alternative source of these enzymes and can provide prospects to overcome these issues. Indeed, marine bacterial dextranases are reportedly more effective and suitable for dental caries prevention and treatment. Here, we focused on properties of dextran, properties of dextran—hydrolyzing enzymes, particularly from marine sources and the biochemical features of these enzymes. Lastly the potential use of these marine bacterial dextranase to remove dental plaque has been discussed. The review covers dextranase-producing bacteria isolated from shrimp, fish, algae, sea slit, and sea water, as well as from macro- and micro fungi and other microorganisms. It is common knowledge that dextranase is used in the sugar industry; produced as a result of hydrolysis by dextranase and have prebiotic properties which influence the consistency and texture of food products. In medicine, dextranases are used to make blood substitutes. In addition, dextranase is used to produce low molecular weight dextran and cytotoxic dextran. Furthermore, dextranase is used to enhance antibiotic activity in endocarditis. It has been established that dextranase from marine bacteria is the most preferable for removing plaque, as it has a high enzymatic activity. This study lays the groundwork for the future design and development of different oral care products, based on enzymes derived from marine bacteria.
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Affiliation(s)
- Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 74576, Iran
- Correspondence: or
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia
| | - Rakesh Das
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 14578, Iran
| | - Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan
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Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123783. [PMID: 35744909 PMCID: PMC9229053 DOI: 10.3390/molecules27123783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.
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Tatli M, Moraïs S, Tovar-Herrera OE, Bomble YJ, Bayer EA, Medalia O, Mizrahi I. Nanoscale resolution of microbial fiber degradation in action. eLife 2022; 11:76523. [PMID: 35638899 PMCID: PMC9191890 DOI: 10.7554/elife.76523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical Clostridium thermocellum system to comprehend how microbes build and use their cellulosomal machinery at these nanometer scales. Degradation of cellulose, the most abundant organic polymer on Earth, is instrumental to the global carbon cycle. We reveal that bacterial cells form ‘cellulosome capsules’ driven by catalytic product-dependent dynamics, which can increase the rate of hydrolysis. Biosynthesis of this energetically costly machinery and cell growth are decoupled at the single-cell level, hinting at a division-of-labor strategy through phenotypic heterogeneity. This novel observation highlights intrapopulation interactions as key to understanding rates of fiber degradation.
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Affiliation(s)
- Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sarah Moraïs
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omar E Tovar-Herrera
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Hengge NN, Mallinson SJB, Pason P, Lunin VV, Alahuhta M, Chung D, Himmel ME, Westpheling J, Bomble YJ. Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus. Int J Mol Sci 2022; 23:ijms23116070. [PMID: 35682749 PMCID: PMC9181691 DOI: 10.3390/ijms23116070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.
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Affiliation(s)
- Neal N. Hengge
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Sam J. B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA 30602, USA;
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
- Correspondence:
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Dowd B, McDonnell D, Tuohy MG. Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.722424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.
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Tan Y, Song W, Gao L, Zhang W, Lu X. Cytophaga hutchinsonii chu_2177, encoding the O-antigen ligase, is essential for cellulose degradation. J Microbiol 2022; 60:364-374. [DOI: 10.1007/s12275-022-1531-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022]
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Fan G, Song W, Guan Z, Zhang W, Lu X. Some novel features of strong promoters discovered in Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2022; 106:2529-2540. [PMID: 35318522 DOI: 10.1007/s00253-022-11869-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Cytophaga hutchinsonii is an important Gram-negative bacterium belonging to the Bacteroides phylum that can efficiently degrade cellulose. But the promoter that mediates the initiation of gene transcription has been unknown for a long time. In this study, we determined the transcription start site (TSS) of C. hutchinsonii by 5' rapid amplification of cDNA ends (5'RACE). The promoter structure was first identified as TAAT and TATTG which are located -5 and -31 bp upstream of TSS, respectively. The function of -5 and -31 regions and the spacer length of the promoter Pchu_1284 were explored by site directed ligase-independent mutagenesis (SLIM). The results showed that the promoter activities were sharply decreased when the TTG motif was mutated into guanine (G) or cytosine (C). Interestingly, we found that the strong promoter was accompanied with many TTTG motifs which could enhance the promoter activities within certain copies. These characteristics were different from other promoters of Bacteriodes species. Furthermore, we carried out genome scanning analysis for C. hutchinsonii and another Bacteroides species by Perl6.0. The results indicated that the promoter structure of C. hutchinsonii possessed more unique features than other species. Also, the screened inducible promoter Pchu_2268 was used to overexpress protein CHU_2196 with a molecular weight of 120 kDa in C. hutchinsonii. The present study enriched the promoter structure of Bacteroidetes species and also provided a novel method for the highly expressed large protein (cellulase) in vivo, which was helpful to elucidate the unique cellulose degradation mechanism of C. hutchinsonii.Key points• The conserved structure of strong promoter of C. hutchinsonii was elucidated.• Two novel regulation motifs of TTTG and AATTATG in the promoter were discovered.• A new method for induced expression of cellulase in vivo was established.• Helpful for explained the unique cellulose degradation mechanism of C. hutchinsonii.
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Affiliation(s)
- Guoqing Fan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Wenxia Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.
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Wang Y, Li L, Xia Y, Zhang T. Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data. FRONTIERS IN BIOINFORMATICS 2022; 2:813771. [PMID: 36304268 PMCID: PMC9580877 DOI: 10.3389/fbinf.2022.813771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
In the era of high-throughput sequencing, genetic information that is inherently whispering hints of the microbes’ functional niches is becoming easily accessible; however, properly identifying and characterizing these genetic hints to infer the microbes’ functional niches remains a challenge. Regarding genome-centric interpretation on the specific functional niche of cellulose hydrolysis for anaerobes, often encountered in practice is a lack of confidence in predicting the anaerobes’ real cellulolytic competency based solely on abundances of the varying carbohydrate-active enzyme modules annotated or on their taxonomy affiliation. Recognition of the synergy machineries that include but not limited to the cellulosome gene clusters is equally important as the annotation of individual carbohydrate-active modules or genes. In the interpretation of complete genomes of 2,768 microbe strains whose phenotypes have been well documented, with the incorporation of an automatic recognition of synergy among the carbohydrate active elements annotated, an explicit genotype–phenotype correlation was evidenced to be feasible for cellulolytic anaerobes, and a bioinformatic pipeline was developed accordingly. This genome-centric pipeline would categorize putative cellulolytic anaerobes into six genotype groups based on differential cellulose-hydrolyzing capacity and varying synergy mechanisms. Suggested in this genotype–phenotype correlation analysis was a finer categorization of the cellulosome gene clusters: although cellulosome complexes, by their nature, could enable the assembly of a number of carbohydrate-active units, they do not certainly guarantee the formation of the cellulose–enzyme–microbe complex or the cellulose-hydrolyzing activity of the corresponding anaerobe strains, for example, the well-known Clostridium acetobutylicum strains. Also, recognized in this genotype-phenotype correlation analysis was the genetic foundation of a previously unrecognized machinery that may mediate the microbe–cellulose adhesion, to be specific, enzymes encoded by genes harboring both the surface layer homology and cellulose-binding CBM modules. Applicability of this pipeline on scalable annotation of large genome datasets was further tested with the annotation of 7,902 reference genomes downloaded from NCBI, from which 14 genomes of putative paradigm cellulose-hydrolyzing anaerobes were identified. We believe the pipeline developed in this study would be a good add as a bioinformatic tool for genome-centric interpretation of uncultivated anaerobes, specifically on their functional niche of cellulose hydrolysis.
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Affiliation(s)
- Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Yu Xia
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- *Correspondence: Tong Zhang,
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35
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Nhim S, Waeonukul R, Uke A, Baramee S, Ratanakhanokchai K, Tachaapaikoon C, Pason P, Liu YJ, Kosugi A. Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9. Appl Microbiol Biotechnol 2022; 106:2133-2145. [PMID: 35157106 PMCID: PMC8930880 DOI: 10.1007/s00253-022-11818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/30/2021] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
Abstract An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC50 = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases. Key points • Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance • A coculture of strain A9 and C. thermocellum showed high cellulose degradation • Strain A9 achieves biological saccharification without addition of β-glucosidase Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11818-0.
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Affiliation(s)
- Sreyneang Nhim
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,Shandong Energy Institute, Qingdao, 266101, People's Republic of China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, People's Republic of China
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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36
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Sharma J, Kumar V, Prasad R, Gaur NA. Engineering of Saccharomyces cerevisiae as a consolidated bioprocessing host to produce cellulosic ethanol: Recent advancements and current challenges. Biotechnol Adv 2022; 56:107925. [DOI: 10.1016/j.biotechadv.2022.107925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 01/01/2023]
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37
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Scheffer G, Rachel NM, Ng KK, Sen A, Gieg LM. Preparation and identification of carboxymethyl cellulose-degrading enzyme candidates for oilfield applications. J Biotechnol 2022; 347:18-25. [DOI: 10.1016/j.jbiotec.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 11/28/2022]
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38
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Sun Q, Raeeszadeh-Sarmazdeh M, Tsai SL, Chen W. Strategies for Multienzyme Assemblies. Methods Mol Biol 2022; 2487:113-131. [PMID: 35687232 DOI: 10.1007/978-1-0716-2269-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
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Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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39
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Sato Y, Takebe H, Oishi K, Yasuda J, Kumagai H, Hirooka H, Yoshida T. Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan. Microbes Environ 2022; 37:ME22039. [PMID: 36273894 PMCID: PMC9763041 DOI: 10.1264/jsme2.me22039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.
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Affiliation(s)
- Yoshiaki Sato
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan,Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Corresponding authors. Yoshiaki Sato: E-mail: ; Tel: +81–28–649–5440. Takashi Yoshida: E-mail: ; Tel: +81–75–753–6217; Fax: +81–75–6226
| | - Hiroaki Takebe
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kazato Oishi
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Jumpei Yasuda
- Iwate Agricultural Research Center Animal Industry Research Institute, Iwate, Japan
| | - Hajime Kumagai
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Hirooka
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Corresponding authors. Yoshiaki Sato: E-mail: ; Tel: +81–28–649–5440. Takashi Yoshida: E-mail: ; Tel: +81–75–753–6217; Fax: +81–75–6226
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40
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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41
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Wei Q, Xia J. Self-Assembled Multienzyme Nanostructures for Biocatalysis in Cellulo. Methods Mol Biol 2022; 2487:197-204. [PMID: 35687238 DOI: 10.1007/978-1-0716-2269-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multienzyme complexes naturally exist in cells to catalyze cascade reactions in metabolic pathways. By clustering the enzymes in close proximity, these nanomachineries achieve effective conversion of metabolites. Bioengineers are working on the development of synthetic versions of multienzyme complexes in cells to synergize heterologous biosynthesis. Assembling enzymes on protein scaffolds through protein-protein interactions is a viable and facile way to form synthetic multienzyme complexes. Here, we describe the general methods to construct self-assembled multienzyme nanostructures in Escherichia coli for biosynthesis of valuable chemicals.
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Affiliation(s)
- Qixin Wei
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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42
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Supplementing Glycerol to Inoculum Induces Changes in pH, SCFA Profiles, and Microbiota Composition in In-Vitro Batch Fermentation. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation8010018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on in vitro fermentation and whether an enhanced buffer capacity of medium could maintain the pH stability during in vitro batch fermentation, subsequently improving the accuracy of short chain fatty acids (SCFAs) determination, especially propionate. Two ileal digesta were fermented by pig fecal inoculum with or without glycerol (served as anti-frozen inoculum or frozen inoculum) in standard buffer or enhanced buffer solution (served as normal or modified medium). Along with the fermentation, adding glycerol decreased the pH of fermentation broth (p < 0.05). However, modified medium could alleviate the pH decrement compared with normal medium (p < 0.05). The concentration of total propionic acid production was much higher than that of other SCFAs in anti-frozen inoculum fermentation at 24 and 36 h, thereby increasing the variation (SD) of net production of propionate. The α-diversity analysis showed that adding glycerol decreased Chao1 and Shannon index under normal medium fermentation (p < 0.05) compared to modified medium (p < 0.05) along with fermentation. PCoA showed that all groups were clustered differently (p < 0.01). Adding glycerol improved the relative abundances of Firmicutes, Anaerovibrio, unclassified_f_Selenomonadaceae, and decreased the relative abundance of Proteobacteria (p < 0.05). The relative abundances of Firmicutes, such as Lactobacillus, Blautia and Eubacterium_Ruminantium_group in modified medium with frozen inoculum fermentation were higher than (p < 0.05) those in normal medium at 36 h of incubation. These results showed that adding glycerol in inoculum changed the fermentation patterns, regardless of substrate and medium, and suggested fermentation using frozen inoculum with modified medium could maintain stability of pH, improve the accuracy of SCFA determination, as well as maintain a balanced microbial community.
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43
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Zhao D, Song W, Wang S, Zhang W, Zhao Y, Lu X. Identification of the Type IX Secretion System Component, PorV (CHU_3238), Involved in Secretion and Localization of Proteins in Cytophaga hutchinsonii. Front Microbiol 2021; 12:742673. [PMID: 34745042 PMCID: PMC8564354 DOI: 10.3389/fmicb.2021.742673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022] Open
Abstract
Cytophaga hutchinsonii can efficiently degrade cellulose and rapidly glide over surfaces, but the underlying mechanisms remain unclear. The type IX secretion system (T9SS) is involved in protein secretion and gliding motility, which is unique to the phylum Bacteroidetes. In this study, we deleted a homologous gene of PorV (chu_3238), a shuttle protein in the T9SS. The Δ3238 mutant caused cellulolytic and gliding defects, while the porV deletion mutants in other Bacteroidetes could glide normally. Adding Ca2+ and K+ improved growth in the PY6 medium, suggesting a potential role of chu_3238 in ion uptake. A proteomic analysis showed an increase in the number of extracellular proteins in the Δ3238 mutant and a decrease in the outer membrane proteins compared to the wild type (WT). Endoglucanase activity in the Δ3238 intact cells was reduced by approximately 70% compared to that of the WT. These results indicate that the secreted proteins could not attach to the cell surface but were released into the extracellular space in the Δ3238 mutant. However, the cargo proteins accumulated in the periplasm of other reported porV deletion mutants. In addition, the homologs of the translocon SprA and a Plug protein were pulled down by co-immunoprecipitation in the 3238-FLAG strain, which are involved in protein transport in the T9SS of Flavobacterium johnsoniae. The integrity of the lipopolysaccharide (LPS) was also affected in the Δ3238 mutant, which may be the reason for the sensitivity of the cell to toxic reagents. The functional diversity of CHU_3238 suggests its important role in the T9SS of C. hutchinsonii and highlights the functional differences of PorV in the T9SS among the Bacteroidetes.
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Affiliation(s)
- Dong Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenxia Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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44
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Pelus A, Bordes G, Barbe S, Bouchiba Y, Burnard C, Cortés J, Enjalbert B, Esque J, Estaña A, Fauré R, Henras AK, Heux S, Le Men C, Millard P, Nouaille S, Pérochon J, Toanen M, Truan G, Verdier A, Wagner C, Romeo Y, Montanier CY. A tripartite carbohydrate-binding module to functionalize cellulose nanocrystals. Biomater Sci 2021; 9:7444-7455. [PMID: 34647546 DOI: 10.1039/d1bm01156a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The development of protein and microorganism engineering have led to rising expectations of biotechnology in the design of emerging biomaterials, putatively of high interest to reduce our dependence on fossil carbon resources. In this way, cellulose, a renewable carbon based polysaccharide and derived products, displays unique properties used in many industrial applications. Although the functionalization of cellulose is common, it is however limited in terms of number and type of functions. In this work, a Carbohydrate-Binding Module (CBM) was used as a central core to provide a versatile strategy to bring a large diversity of functions to cellulose surfaces. CBM3a from Clostridium thermocellum, which has a high affinity for crystalline cellulose, was flanked through linkers with a streptavidin domain and an azide group introduced through a non-canonical amino acid. Each of these two extra domains was effectively produced and functionalized with a variety of biological and chemical molecules. Structural properties of the resulting tripartite chimeric protein were investigated using molecular modelling approaches, and its potential for the multi-functionalization of cellulose was confirmed experimentally. As a proof of concept, we show that cellulose can be labelled with a fluorescent version of the tripartite protein grafted to magnetic beads and captured using a magnet.
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Affiliation(s)
- Angeline Pelus
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Gaëlle Bordes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Sophie Barbe
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Younes Bouchiba
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Callum Burnard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Brice Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Jeremy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Anthony K Henras
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Stéphanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Claude Le Men
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | | | - Julien Pérochon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Marion Toanen
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Amandine Verdier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Camille Wagner
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Yves Romeo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
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Rubio-Portillo E, Martin-Cuadrado AB, Ramos-Esplá AÁ, Antón J. Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes). mSystems 2021; 6:e0086621. [PMID: 34519521 PMCID: PMC8547425 DOI: 10.1128/msystems.00866-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | | | - Alfonso Ángel Ramos-Esplá
- Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
- CIMAR, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
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Sanjaya RE, Putri KDA, Kurniati A, Rohman A, Puspaningsih NNT. In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies. J Genet Eng Biotechnol 2021; 19:143. [PMID: 34591195 PMCID: PMC8484414 DOI: 10.1186/s43141-021-00236-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. RESULTS The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332-751 amino acids, with the molecular weight range around 37-83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. CONCLUSION This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.
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Affiliation(s)
- Rahmat Eko Sanjaya
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Chemistry Education Study Program, Faculty of Teacher Training and Education, Universitas Lambung Mangkurat, Jl. Brigjend. H. Hasan Basry, Banjarmasin, Kalimantan, 70123, Indonesia
| | - Kartika Dwi Asni Putri
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Anita Kurniati
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Health, Faculty of Vocational Studies, Kampus B Universitas Airlangga, Surabaya, East Java, 60286, Indonesia
| | - Ali Rohman
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
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Ko HJ, Song H, Choi IG. Development of a Novel Cell Surface Attachment System to Display Multi-Protein Complex Using the Cohesin-Dockerin Binding Pair. J Microbiol Biotechnol 2021; 31:1183-1189. [PMID: 34226404 PMCID: PMC9705933 DOI: 10.4014/jmb.2105.05022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Autodisplay of a multimeric protein complex on a cell surface is limited by intrinsic factors such as the types and orientations of anchor modules. Moreover, improper folding of proteins to be displayed often hinders functional cell surface display. While overcoming these drawbacks, we ultimately extended the applicability of the autodisplay platform to the display of a protein complex. We designed and constructed a cell surface attachment (CSA) system that uses a noncovalent protein-protein interaction. We employed the high-affinity interaction mediated by an orthogonal cohesin-dockerin (Coh-Doc) pair from Archaeoglobus fulgidus to build the CSA system. Then, we validated the orthogonal Coh-Doc binding by attaching a monomeric red fluorescent protein to the cell surface. In addition, we evaluated the functional anchoring of proteins fused with the Doc module to the autodisplayed Coh module on the surface of Escherichia coli. The designed CSA system was applied to create a functional attachment of dimeric α-neoagarobiose hydrolase to the surface of E. coli cells.
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Affiliation(s)
- Hyeok-Jin Ko
- Food Biotech R&D Center, Samyang Corp., Seongnam 13488, Republic of Korea
| | - Heesang Song
- Department of Biochemistry and Molecular Biology, Chosun University School of Medicine, Gwangju 61452, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Cheawchanlertfa P, Tongsuk P, Sutheeworapong S, Waeonukul R, Pason P, Poomputsa K, Ratanakhanokchai K, Kosugi A, Tachaapaikoon C. A novel amylolytic/xylanolytic/cellulolytic multienzyme complex from Clostridium manihotivorum that hydrolyzes polysaccharides in cassava pulp. Appl Microbiol Biotechnol 2021; 105:6719-6733. [PMID: 34436648 DOI: 10.1007/s00253-021-11521-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
Some anaerobic bacteria, particularly Clostridium species, produce extracellular cellulolytic and xylanolytic enzymes as multienzyme complexes (MECs). However, an amylolytic/xylanolytic/cellulolytic multienzyme complex (AXC-MEC) from anaerobic bacteria is rarely found. In this work, the glycoprotein AXC-MEC, composed of subunits of amylolytic, xylanolytic, and cellulolytic enzymes, was isolated from crude extracellular enzyme of the mesophilic anaerobic bacterium Clostridium manihotivorum CT4, grown on cassava pulp, using a milled cassava pulp column and Sephacryl S-500 gel filtration chromatography. The isolated AXC-MEC showed a single band upon native-polyacrylamide gel electrophoresis (native-PAGE). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed at least eight protein bands of the multienzyme complex which predominantly exhibited amylolytic enzyme activity, followed by xylanolytic and cellulolytic enzyme activities. The AXC-MEC is highly capable of degrading starch and non-starch polysaccharides present in cassava pulp into glucose and oligosaccharides, without conventional pretreatment. Base on the genomic analysis of C. manihotivorum CT4, we found no evidence of the known structural components of the well-known multienzyme complexes from Clostridium species, cellulosomes such as scaffoldin, cohesin, and dockerin, indicating that AXC-MEC from strain CT4 exhibit a different manner of assembly from the cellulosomes. These results suggest that AXC-MEC from C. manihotivorum CT4 is a new MEC capable of hydrolyzing cassava pulp into value-added products, which will benefit the starch industry. KEY POINTS: • Glycoprotein AXC-MEC was first reported in Clostridium manihotivorum. • Unlike cellulosomes, AXC-MEC consists of amylase, xylanase, and cellulase. • Glucose and oligosaccharides were hydrolysis products from cassava pulp by AXC-MEC.
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Affiliation(s)
- Pattsarun Cheawchanlertfa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Pornpimon Tongsuk
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Sawannee Sutheeworapong
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand. .,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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49
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Gao G, Cao J, Mi L, Feng D, Deng Q, Sun X, Zhang H, Wang Q, Wang J. BdPUL12 depolymerizes β-mannan-like glycans into mannooligosaccharides and mannose, which serve as carbon sources for Bacteroides dorei and gut probiotics. Int J Biol Macromol 2021; 187:664-674. [PMID: 34339781 DOI: 10.1016/j.ijbiomac.2021.07.172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022]
Abstract
Symbiotic bacteria, including members of the Bacteroides genus, are known to digest dietary fibers in the gastrointestinal tract. The metabolism of complex carbohydrates is restricted to a specified subset of species and is likely orchestrated by polysaccharide utilization loci (PULs) in these microorganisms. β-Mannans are plant cell wall polysaccharides that are commonly found in human nutrients. Here, we report the structural basis of a PUL cluster, BdPUL12, which controls β-mannan-like glycan catabolism in Bacteroides dorei. Detailed biochemical characterization and targeted gene disruption studies demonstrated that a key glycoside hydrolase, BdP12GH26, performs the initial attack on galactomannan or glucomannan likely via an endo-acting mode, generating mannooligosaccharides and mannose. Importantly, coculture assays showed that the B. dorei promoted the proliferation of Lactobacillus helveticus and Bifidobacterium adolescentis, likely by sharing mannooligosaccharides and mannose with these gut probiotics. Our findings provide new insights into carbohydrate metabolism in gut-inhabiting bacteria and lay a foundation for novel probiotic development.
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Affiliation(s)
- Ge Gao
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiawen Cao
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lan Mi
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dan Feng
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Deng
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobao Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huien Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Qian Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jiakun Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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50
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Hou Y, Sun X, Dou M, Lu C, Liu J, Rao W. Cellulose Nanocrystals Facilitate Needle-like Ice Crystal Growth and Modulate Molecular Targeted Ice Crystal Nucleation. NANO LETTERS 2021; 21:4868-4877. [PMID: 33819045 DOI: 10.1021/acs.nanolett.1c00514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ice nucleators are of crucial and important implications in various fields including chemistry, climate, agriculture, and cryobiology. However, the complicated extract and biocompatibility of ice nucleators remain unresolved, and the mechanism of ice nucleation remains largely unknown. Herein, we show that natural nanocrystalline cellulose materials possess special properties to enhance ice nucleation and facilitate needle-like ice crystal growth. We reveal the molecular level mechanism that the efficient exposure of cellulose hydroxyl groups on (-110) surface leads to faster nucleation of water. We further design chitosan-decorated cellulose nanocrystals to accomplish molecular cryoablation in CD 44 high-expression cells; the cell viability shows more than ∼10 times decrease compared to cryoablation alone and does not show evident systematic toxicity. Collectively, our findings also offer improved knowledge in molecular level ice nucleation, which may benefit multiple research communities and disciplines.
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Affiliation(s)
- Yi Hou
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuyang Sun
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Mengjia Dou
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chennan Lu
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Wei Rao
- Beijing Key Lab of CryoBiomedical Engineering and Key Lab of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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